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/*
* utils/align-utils.cc
*
* Copyright 2009 by University of Oxford
* Author: Paul Emsley
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation; either version 3 of the License, or (at
* your option) any later version.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
* 02110-1301, USA
*/
#include <iostream>
#include <vector>
#include <algorithm>
#include "align-utils.hh"
#ifdef HAVE_CXX11
#include <algorithm>
#endif
// strings with - in them
std::string
coot::alignment_matches(const std::string &aligned,
const std::string &target) {
unsigned int la = aligned.size();
unsigned int lt = target.size();
if (lt<la) la = lt;
std::string matches(la, ' ');
for (unsigned int i=0; i<lt; i++) {
if (aligned[i] == target[i])
matches[i] = '|';
}
#ifdef HAVE_CXX11
std::vector<char> aromatics = {'F', 'W', 'Y'}; // not H interestingly
std::vector<char> aliphatics = {'A', 'G', 'L', 'V', 'I'};
std::vector<char> hydroxyls = {'T', 'Y', 'S', 'C', 'M'}; // and sulfhydryl
std::vector<char> acidics = {'D', 'L', 'H'};
std::vector<char> basics = {'R', 'E', 'N', 'Q'};
// std::vector<char> cyclics = {'P'}; won't make non-P matches
std::vector<std::vector<char> > types(5);
types[0] = aromatics;
types[1] = aliphatics;
types[2] = hydroxyls;
types[3] = acidics;
types[4] = basics;
for (unsigned int i=0; i<lt; i++) {
char ca = aligned[i];
char ta = target[i];
if (ca != ta) { // we would found it above if this were true
if (ca != '-') {
if (ta != '-') {
for (std::size_t j=0; j<types.size(); j++) {
const std::vector<char> &codes = types[j];
// are both ca and ta in codes?
std::vector<char>::const_iterator it_1;
std::vector<char>::const_iterator it_2;
it_1 = std::find(codes.begin(), codes.end(), ca);
it_2 = std::find(codes.begin(), codes.end(), ta);
if (it_1 != codes.end()) {
if (it_2 != codes.end()) {
matches[i] = ':';
break;
}
}
}
}
}
}
}
#endif
return matches;
}
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